Multidrug-resistant organism co-colonization in patients with discordant direct stool Xpert Carba-R and culture-based carbapenemase-producing Enterobacterales surveillance results

Discrepancies between direct molecular surveillance and culture-based surveillance for carbapenemase-producing Enterobacterales (CPE) complicate infection control decision-making. This study investigated co-colonization patterns of multidrug-resistant organisms (MDROs) in patients with discordant results. From March to December 2023, two rectal swabs were simultaneously collected from high-risk patients at a tertiary hospital: one for direct Xpert Carba-R assay and one for culture-based molecular assay. Among 4120 screened patients, 142 (3.4%) tested positive by direct molecular assay, of whom 49 (34.5%) showed discordant results. Discordance included culture-negative patients (n = 38) and patients with different carbapenemase genes detected between methods (n = 11). Among 38 culture-negative patients, 14 (36.8%) harbored MDROs from clinical specimens: multidrug-resistant Pseudomonas aeruginosa (MRPA) (n = 9, 23.7%), multidrug-resistant Acinetobacter baumannii (n = 2, 5.3%), CPE (n = 2, 5.3%), and vancomycin-resistant enterococci (n = 1, 2.6%). For gene-level analysis, each unconfirmed carbapenemase gene was analyzed separately, yielding 51 discordant detections from 49 patients. Discordant bla_NDM detection (n = 27) was associated with MRPA isolation compared to other carbapenemase genes (11/27, 40.7%, P = 0.018), predominantly from respiratory and urinary specimens. Median time from surveillance to MDRO detection was 2 days (IQR 0.5–6.5). Positive direct molecular CPE results indicate a broader MDRO burden, supporting consideration of comprehensive infection control measures even when culture results are negative.